I just tested the Simulation package and the software worked quite nice. Now it's time to publish the data of backbon RMSD together with Time (ps) like this:

http://www.biomedcentral.com/content/figures/1471-2164-11-S4-S25-9.jpg

I used the "Analyze Trajectory" module to calculate the backbone RMSD but the plot created look awful (There are only 170 frames created so there are only 170 spots on the graph) .Please show us how to make a nice image like the one I posted. Thanks for your support.